ChEMBL Resources

Wednesday, 22 October 2014

myChEMBL 19 Released

We are very pleased to announce that the latest myChEMBL release, based on the ChEMBL 19 database, is now available to download. In addition to the extra data, you will also find a number a great new features. So what's new then?

More core chemoinformatics tools

We have included OSRA (Optical Structure Recognition), which is useful for extracting compound structures from images. OSRA can be accessed from the command line or by very convenient web interface, provided by Beaker (described below). We've also added OpenBabel - another great open source cheminformatics toolkit. This means you can now experiment with both RDKit and OpenBabel and use whichever you prefer.

ChEMBL Beaker

myChEMBL now ships with a local instance the ChEMBL Beaker service. For those not familiar with Beaker, the service provides users with an array of chemoinformatics utilities via a RESTful API. Under the hood, Beaker is using RDKit and OSRA to carry out its methods. With the addition of Beaker in myChEMBL, users can now carry out the following tasks in secure local environment:

Convert chemical structure bewteen multiple formats

Extract compound information from images and pdfs

Generate compound images in raster (png) and vector (svg) forms

Generate HTML5 ready representation of compound structure

Generate compound fingerprints

Generate compound descriptors

Identify Maximum Common Substructure

Compound standardisation

Lots of more calculations

New IPython notebooks

We have written a number of new IPyhthon notebooks, which focus on a range of cheminformatics and bioinformatic topics. The topics covered by the new notebooks include:

Future plans

The myChEMBL resource is an evolving system and we are always looking to add new open source projects, tools and notebooks. We would be really interested to hear from users about what they would like to see in future myChEMBL releases, so please get in touch if you have any suggestions. (Just so you know, we already have a couple of ideas for myChEMBL 20).

We hope you find this myChEMBL update useful and if you spot any issues or have any questions let us know.

Sorry to hear you are having problems with the install. If you have time maybe you could send some more details to 'mychembl at ebi.ac.uk'. One thing we did notice recently, which caused a similar issue to what you describe was the 'Adapter Type' in the Advanced network settings was set to a server version - it should be changed to the desktop equivalent, something like 'Intel PRO/1000 MT Desktop'.